rs9304489

chr18-26079235-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001007559.3(SS18):c.147-1075G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,130 control chromosomes in the GnomAD database, including 5,784 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.19 (5784 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: SS18 NM_001007559.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

SS18 (HGNC:11340): (SS18 subunit of BAF chromatin remodeling complex) Enables nuclear receptor coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Part of SWI/SNF complex. Implicated in synovial sarcoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SS18	NM_001007559.3	c.147-1075G>A		intron_variant		ENST00000415083.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SS18	ENST00000415083.7	c.147-1075G>A		intron_variant		1	NM_001007559.3	A1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29190 AN: 152012 Hom.: 5768 Cov.: 33

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.167

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.192 AC: 29255 AN: 152130 Hom.: 5784 Cov.: 33 AF XY: 0.189 AC XY: 14067 AN XY: 74384

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0937

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.0461

Gnomad4 OTH AF: 0.165

Alfa AF: 0.137 Hom.: 613

Bravo AF: 0.220

Asia WGS AF: 0.160 AC: 556 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.8
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9304489; hg19: chr18-23659199;